Dear Dr. Justin Thank you for the insight . My problem is solved.
Best Agnivo Gosai Graduate Student Mechanical Engineering Iowa State University On Sat, Aug 9, 2014 at 5:00 AM, < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > > 1. Re: Charmm to gromacs (Justin Lemkul) > 2. Re: Can I delete trr file? (Justin Lemkul) > 3. Re: Can we set the number of pure PME nodes when using > GPU&CPU? (Theodore Si) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 09 Aug 2014 03:39:07 -0600 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Charmm to gromacs > Message-ID: <53e5ec3b.4070...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > On 8/8/14, 9:18 PM, Abu Naser wrote: > > > > > > > > Thanks Justin for your response. > > > > I just manually inserted the input values only to that part of the > script. The atom types I am interested in, they are not available in the > charmm36. Since I have only few unusual atom types, I wish to do them > manually and trying to figure out how it can be converted. > > > > It appears that the script uses the C6/C12 approach instead of specifying > sigma > and epsilon. That is not how we converted the CHARMM36 files. The > conversion > factors are a simple matter of units. Epsilon is in kcal/mol and needs to > be in > kJ/mol, so multiply by 4.184 (and by -1 since CHARMM specifies these > values as > negative, but Gromacs uses a different convention). For sigma, CHARMM > specifies > Rmin/2 directly, but can be converted by multiplying by 2 (to get Rmin), > then > multiplying by 2^(-1/6) (to get sigma), then multiplying by 0.1 (to > convert A->nm). > > -Justin > > > > > > > > > > > > > > > > > > >> Date: Fri, 8 Aug 2014 08:50:16 -0600 > >> From: jalem...@vt.edu > >> To: gmx-us...@gromacs.org > >> Subject: Re: [gmx-users] Charmm to gromacs > >> > >> > >> > >> On 8/8/14, 3:11 AM, Abu Naser wrote: > >>> Hi All, > >>> > >>> I took the following from Mark's script to convert non-bonded > parameters of ZN manually: > >>> > >>> printf("% 5s %f 0.0 A %.4g %.4g\n", $atom, $element_mass, > 2*$four_epsilon * $sigma**6, $four_epsilon * $sigma**12); > >>> > >>> > >>> I am getting: > >>> > >>> -0.0002245 -1.205e-08 > >>> > >>> instead of: > >>> > >>> 0.194215920555 1.046 > >>> > >>> > >>> Am I missing anything? > >>> > >>> I would appreciate your respond. > >>> > >> > >> Probably something wrong with your input file. There's no need to do > these > >> conversions; we provide the latest CHARMM36 FF for Gromacs at > >> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs > >> > >> -Justin > >> > >> -- > >> ================================================== > >> > >> Justin A. Lemkul, Ph.D. > >> Ruth L. Kirschstein NRSA Postdoctoral Fellow > >> > >> Department of Pharmaceutical Sciences > >> School of Pharmacy > >> Health Sciences Facility II, Room 601 > >> University of Maryland, Baltimore > >> 20 Penn St. > >> Baltimore, MD 21201 > >> > >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 > >> http://mackerell.umaryland.edu/~jalemkul > >> > >> ================================================== > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > > > > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > > > ------------------------------ > > Message: 2 > Date: Sat, 09 Aug 2014 03:40:17 -0600 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org, Batdorj Batsaikhan > <batsaikhan...@yahoo.com> > Subject: Re: [gmx-users] Can I delete trr file? > Message-ID: <53e5ec81.2070...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > On 8/8/14, 10:58 PM, Batdorj Batsaikhan wrote: > > Dear gmx users, > > > > I am new user of gromacs. Our calculations are running, but we have a > problem that has not enough disk space. Therefore I need to delete some > file that are unimportant for analysis. Is there any analysis use trr file? > Can I delete trr file? > > > > Not while mdrun is running; that will kill the run. The most important > part of > the run is the trajectory, so if you delete the .trr you'd better have the > .xtc > as well, otherwise there was no point in doing the simulation. Better > planning > (in terms of frequency for saving frames) and paying attention to what > grompp > tells you about how much data will be generated pay off here. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > > > ------------------------------ > > Message: 3 > Date: Sat, 09 Aug 2014 17:56:47 +0800 > From: Theodore Si <sjyz...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Can we set the number of pure PME nodes when > using GPU&CPU? > Message-ID: <53e5f05f.70...@gmail.com> > Content-Type: text/plain; charset=windows-1252; format=flowed > > Hi, > > You mean no matter we use GPU acceleration or not, -npme is just a > reference? > Why we can't set that to a exact value? > > On 8/9/2014 5:14 AM, Mark Abraham wrote: > > You can set the number of PME-only ranks with -npme. Whether it's useful > is > > another matter :-) The CPU-based PME offload and the GPU-based PP offload > > do not combine very well. > > > > Mark > > > > > > On Fri, Aug 8, 2014 at 7:24 AM, Theodore Si <sjyz...@gmail.com> wrote: > > > >> Hi, > >> > >> Can we set the number manually with -npme when using GPU acceleration? > >> > >> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at http://www.gromacs.org/ > >> Support/Mailing_Lists/GMX-Users_List before posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > > > > ------------------------------ > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > > End of gromacs.org_gmx-users Digest, Vol 124, Issue 40 > ****************************************************** > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.